Expression data from mouse wild-type and Dnmt1-/-Dnmt3a-/-Dnmt3b-/- embryonic stem(ES) cells and nuclear transfer-trophoblastic stem(ntTS) cells, and wild-type trophoblastic stem(TS) cells, primitive endoderm cells, and extra-embryonic endoderm(XEN) cells

To investigate the role of DNA methylation in early embryogenesis, we created Dnmt1-/-Dnmt3a-/-Dnmt3b-/- triple knockout (TKO) embryos by the nuclear transfer (NT) technique using TKO ES cells as the nucleus donor, and found that the TKO NT embryos could develop into blastocysts. From the TKO NT blastocysts, we successfully established trophoblastic stem cells (ntTS cells), and these TKO ntTS cells could self-renew and contribute to the placenta in vivo. Expression profile analysis using microarray revealed that, although many genes were aberrantly expressed, the fundamental gene expression patterns of stem cells were retained in these TKO ntTS cells. To investigate the properties of the TKO ntTS cells from their expression profiles, we compared the microarray data from the TKO ntTS cells with data from wild-type (WT) ntTS cells and other cell types that represent the three blastocyst-derived lineages: the epiblast (EPI), trophectoderm (TE), and primitive endoderm (PE). WT and TKO ES cells were used as EPI, TS cells derived from wild-type blastocysts were used as TE, and extra-embryonic endoderm (XEN) cells derived from wild-type blastocysts were used as PE. We also treated WT ES cells with Gata4 to induce parietal endoderm cells as PE. The total RNA was extracted from these cell lines, and microarray data were obtained using mouse expression microarrays.